Commit 4375a55d authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Switched to InProcessFunction, no cluster job needed for ln commands

parent 8cf28116
package nl.lumc.sasc.biopet.wrappers
import nl.lumc.sasc.biopet.core._
import org.broadinstitute.sting.queue.function.CommandLineFunction
//import org.broadinstitute.sting.queue.function.QFunction
import org.broadinstitute.sting.queue.function.InProcessFunction
import org.broadinstitute.sting.commandline._
import java.io.File
import scala.sys.process._
class Ln(val globalConfig: Config) extends CommandLineFunction {
class Ln(val globalConfig: Config) extends InProcessFunction {
def this() = this(new Config(Map()))
this.analysisName = "ln"
val config: Config = Config.mergeConfigs(globalConfig.getAsConfig(analysisName), globalConfig)
logger.debug("Config for " + this.analysisName + ": " + config)
@Input(doc="Input file") var in: File = _
@Output(doc="Link destination") var out: File = _
def commandLine = {
"ln -sf " + required(in) + required(out)
override def run {
val cmd = "ln -s " + in + " " + out
val exitcode = cmd.!
System.out.println("cmd: '" + cmd + "', exitcode: " + exitcode)
}
}
object Ln {
def addLn(input:File, output:File) : Ln = {
return new Ln { this.in = input; this.out = output }
}
}
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